PDBsum entry 2vqh

Membrane protein

PDB id: 2vqh

Contents

Protein chains

76 a.a. *

72 a.a. *

Ligands

CAC ×3

Metals

_ZN ×8

* Residue conservation analysis

PDB id:

2vqh

Name:

Membrane protein

Title:

Crystal structure of porb from corynebacterium glutamicum (crystal form ii)

Structure:

Putative uncharacterized protein cgl0972. Chain: a, b. Fragment: residues 28-126. Synonym: porb, anion-specific porin, anion-specific porin precursor. Engineered: yes

Source:

Corynebacterium glutamicum. Organism_taxid: 1718. Atcc: 13032. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.89Å R-factor: 0.247 R-free: 0.256

Authors:

K.Ziegler,R.Benz,G.E.Schulz

Key ref:

K.Ziegler et al. (2008). A putative alpha-helical porin from Corynebacterium glutamicum. J Mol Biol, 379, 482-491. PubMed id: 18462756 DOI: 10.1016/j.jmb.2008.04.017

Date:

15-Mar-08 Release date: 20-May-08

Protein chain

Q8NRS3  (Q8NRS3_CORGL) -  PorB from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)

Seq: 126 a.a.

Struc: 76 a.a.

Protein chain

Q8NRS3  (Q8NRS3_CORGL) -  PorB from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)

Seq: 126 a.a.

Struc: 72 a.a.

DOI no: 10.1016/j.jmb.2008.04.017

J Mol Biol 379:482-491 (2008)

PubMed id: 18462756

A putative alpha-helical porin from Corynebacterium glutamicum.

K.Ziegler, R.Benz, G.E.Schulz.

ABSTRACT

The cell wall of Corynebacterium glutamicum contains a mycolic acid layer, which is a protective nonpolar barrier similar to the outer membrane of Gram-negative bacteria. The exchange of material across this barrier requires porins. Porin B (PorB) is one of them. Recombinant PorB has been produced in Escherichia coli, purified, crystallized and analyzed by X-ray diffraction, yielding 16 independent molecular structures in four different crystal forms at resolutions up to 1.8 A. All 16 molecules have the same globular core, which consists of 70 residues forming four alpha-helices tied together by a disulfide bridge. The 16 structures vary greatly with respect to the 29 residues in the N- and C-terminal extensions. Since corynebacteria belong to the group of mycolata that includes some prominent human pathogens, the observed structure may be of medical relevance. Due to the clearly established solid structure of the core, the native porin has to be oligomeric, and the reported structure is one of the subunits. An alpha-helical porin in a bacterial outer envelope is surprising because all presently known structures of such porins consist of beta-barrels. Since none of the four crystal packing arrangements was compatible with an oligomeric membrane channel, we constructed a model of such an oligomer that was consistent with all available data of native PorB. The proposed model is based on the required polar interior and nonpolar exterior of the porin, on a recurring crystal packing contact around a 2-fold axis, on the assumption of a simple C(n) symmetry (a symmetric arrangement around an n-fold axis), on the experimentally established electric conductivity and anion selectivity and on the generally observed shape of porin channels.

Selected figure(s)

Figure 2.
Fig. 2. Stereoview of PorB molecule Ia of crystal form I showing the C^α backbone with side chains and disulfide bridge. The backbone of the 70-residue core structure is shown in orange. The extensions with unreliable conformations are shown in green. The strictly conserved side chains are shown in orange as well (Fig. 4). Some residues are labeled.

Figure 5.
Fig. 5. Stereoviews of the pentameric model of native porin. (a) Modeled contact showing the three calcium ions at their assigned sites (green). (b) C^α plot of the general construction. The 17 N-terminal and 12 C-terminal residues (Fig. 4) from adjacent subunits have no defined structure in the crystal and most likely associate with each other (dotted lines). (c) View along the 5-fold axis showing the intersubunit salt bridge Arg42–Asp87′. The five PorB core structures are given as inflated stick models, as in Fig. 3. The peptide of the N- and C-terminal extensions is indicated by transparent balls with volumes corresponding to the missing mass. (d) View of the tilted channel showing the calcium ions (green). The intersubunit salt bridge Glu36–Arg77′ at the outer surface explains the strong conservation of both residues (Fig. 4).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 379, 482-491) copyright 2008.

Figures were selected by the author.